Fishermen will be given access to premium markets in exchange for switching to fishing methods that have a lower impact on marine life.
The Blue Marine Foundation, which is behind the project, will shortly name the areas. But Sky News understands they will stretch from the Channel Islands to Scotland.
The voluntary system, agreed between the charity and local conservationists and fishermen, has been hugely successful in Lyme Bay, Dorset.
A decade ago the area, known as England's coral garden, was being destroyed by heavy fishing gear that ripped up the reef.
But the fishery has bounced back by banning bottom trawling, laying crab pots away from the reef and using nets that allow juvenile fish and non-target species to escape.
Scallop and crab landings have doubled, and there has been a four-fold increase in the number of species inhabiting the reef.
In return, the foundation provides harbour-side chillers to keep the fish fresh and a sustainability stamp that means the catch is in demand from top-end restaurants.
Mandy Wolfe, Lyme Bay Reserve coordinator for the Blue Marine Foundation, said: "It's a win, win, win, because it's less fishing, bigger catches and better prices for them."
Aubrey Banfield, who has been fishing in Lyme Bay for seven years, said reaching an agreement had been tricky, particularly with life-long fishermen who were reluctant to change.
"There were a lot of fights at first, but compromises were made and it just works," he told Sky News.
Lewis Pugh, who has been swimming the length of the English Channel to highlight poor marine protection, said: "The most surprising thing about this swim has been how little, in terms of wildlife, I have seen in the English Channel.
"I would urge the UK government to have a very hard look at its fisheries policy and to do everything that they can to ensure that it is sustainable, because if you don't, there will be nothing left for our future and that's for our children and our grandchildren."